Posted
by
Zonk
on Thursday June 02, 2005 @10:55AM
from the mix-your-own-nematode dept.

pafischer writes "Forbes is reporting on a Biotech startup company trying to make DNA manipulation as easy as Photoshop. From the article: 'The goal is to move from having to merely tweak the proteins that are used as biotech drugs to being able to design them, even taking material from multiple organisms and using them to create new, functional genes.'"

Slightly OT, but one of my favorite pinball machines is the South Park machine. One of the game objectives is to hit targets to increase your number of asses on your monkey. Each time you hit the target in the bonus phase, the machine cries out "[x] ASS MONKEY"

Mark me as a FOB (Fan of Bill), but kudos to him and his foundation for their contribution to science...

Of course, he has a motive. He's donating money to help develop a user-friendly gene manipulation tool in hopes that it will cut into the market of the Open Source gene manipulation. Then, when people become dependent on the new gene manipulation, Microsoft will buy the company and merge it with their next version of windows, leaving geeks as the only ones doing gene manipulation the old way (by hand

Also, does the good they do outweigh the harm they do to society? Doubtful. It's equally doubtful for most super-rich men. I think it's a way to ease their conscience about all the horrible things they've done.

I'd be interested to hear how you think Microsoft's antitrust violations are more significant than the hundreds of millions of dollars the B&M Gates foundation donates to AIDS research, education, health initiatives, and technology.

The title of the linked article is the only part that even mentions Photoshop. Nowhere in the article does anyone claim that the process would be as easy as using Photoshop, or any other software programming.

They do compare the advance in genetic manipulation to the difference between editing with Wite-Out and editing with a word processor, but that's what we call an analogy. They're not claiming that producing genes would be something anyone with no training can do with their home computer.

Currently, it's easy to 1) amplify large chunks of DNA verbatim and 2) change individual nucleotides. What is difficult is making large blocks of novel or heavily modified sequence, as it's expensive or impossible to synthesize them from nucleotides. Codon Devices seems to have a way to generate large chunks of customized sequence.

How important that turns out to be, we'll see, but the company does have some really smart people behind it. Anyway, that's how I understand

Being able to make long synthetic DNA sequences would be immensely valuable. Right now practicality limits synthtic DNA to less than 100 bases. Genes are kilobases long even in bacteria. You need megabases for animals if you want to keep the introns intact (scary - a single animal gene can approach an entire bacterial genome in length).

What the article lacks is one critical detail - how exactly they plan on doing all this.

Imagine I started a new company designed to revolutionize computing, pointing out

I must say I'm impressed! Put all this in a black box and sell it for $100k and it will do for DNA systhesis what the ABI 770 (or whatever the model number is) did for sequencing... I can picture libraries of clones with every possible single- and double-mutant of a moderate-size protein - that would have endless uses...

They are writing a program to compute the results of manipulating genes. How does that relate to photoshop, other than there will probably be a picture you edit using your mouse. That is like saying Autocad and Photoshop are the same since you are creating pretty pictures in both.

If they pull this off, it has way more to do with biology and math than the interface they use. Not to mention that even if this application simulates gene manipulation, they will still have to do the same thing by hand to tes

And as OS races to catch up with this new Photoshop feature can you imagine some of the freaks that will be created at people struggle with the GIMPs interface. Now I understand why they called it gimp.

Designing DNA to create a given protein is no big deal. The hardest problem is figuring out how the new gene/protein will act inside the organism. Biological systems don't have a nice layered OSI model for what connects to what -- its like nearly everything is a global-accessible variable so side-effects are a real problem. New drugs require huge amounts of R&D in the testing phase, not the synthesis phase.

I'd be more impressed if someone created an accurate in silico system for testing new drugs, rather than just designing new DNA sequences that MIGHT make useful new proteins that MIGHT make a useful new drug.

Designing DNA to create a given protein sequence is no big deal. Designing a new sequence to yield a desired structure is a huge problem, which has only be solved for special cases - google the "protein folding problem". Designing a structure with a desired function is practically impossible at the current level of theoretical knowledge. If we have solved all of that, then we might think about interactions in the organism. Nearly no drug design is done by rational approaches today, it is all mass screening.

Don't worry too much. They'll get shut down by Homeland Security as soon as it becomes obvious that terrorists could splice'n'dice some *really* nasty bugs. Not just biological warfare, either. Imagine someone cooking up an organism that craps plastic explosive... Drop that in a bag of sugar along with a bug that decomposes exothermically after a predetermined time. Hmmm.... Could bake up some Combat Muffins (apologies to pterry). Good times.

Guys, with the new GTA:DNA, you can walk up to a sexy celebrity stud and jack their DNA. You too can be a vapid, overpaid prick and have television cameras point at you when you babble senselessly about geopolitical paradigms of which you lack even a basic conceptual understanding!

Gals, with GTA:DNA, you can walk up to a sexy celebrity starlet and, well, actually, all you can do is find out what they really look like under all that make up, plastic surgery, silicone, botox and advanced composite material

In fact, a friend of mine did two major variants just this quarter at the Baker labs down the hall, one with a luminescent rocker switch and one with a ligand-activated toggle.

Just making it all pretty doesn't mean you know what it will do. It's more important to understand how it will work and how the whole chain will be impacted than it does being able to just visualize it.

It's just that step one is literally so obvious that you could ask a kid. And step 2 is so notoriously complex that I don't expect this company to amount to anything more than a plughole for research grants.

in the hands of the wrong person, this allows any idiot to design a better plague. Why do people always see these things in the light of how it will be GOOD and never the downside. Do we really need easier bioterrorism?

Like most advances in biotechnology, "any idiot" has no hope of using the technique (whatever the hell it actually is). Heck, half the molecular biologists out there will be incapable of using it properly if it's anything like other research tools.

And one more thing... this is all expensive. Very, very expensive. Even a basic (and I mean BASIC, as in you could maybe do three experiments) molecular bio lab starts at many tens of thousands of dollars. That's with teaching grade supplies and equipment, no

BUT all those people bent on doing it will have that much easier a time as well. Terrorists seem to be well funded and this lowers the bar from the person needed being a one of a kind researcher to a one in a million person. it DOES make it more achieveable

The first thing I thought of is how this might affect DNA used in criminal cases. If it becomes simple to manipulate DNA, would it be possible for a forensic analyst to, say, grease the wheels a bit on finding the "right" DNA on a particular item? It seems that if the DNA on an object were manipulated to mirror another's DNA, the switch wouldn't be so easily traceable. Then again, the analyist could always clean the item and tamper with it in a variety of other ways too.

Unless all they plan to produce is pretty pictures of DNA... I wonder if it will incorporate the physical and chemical properties of the agents or will they just be able to string together whatever sequences they want?

I agree that genes should be left for geneticists, but when your compiler, debugger, and emmulator/simulator check for bad or even icky results, it might actually be fun to toy with genes, in an neat visual way.

At least, I have fantasies about modifying vegetables, fruits, and bugs. I expect that wasps can be reengineered to produce complete reams of laser printer paper, even with a sealed paper wrapper. I expect that ants or cockroaches could be modified to clean your house, better than they do. I expect bacteria or other small folded shapes can be reengineered to spit-out carbon nanotubes, construct simple buildings, or eat trash and grow fuel-cell cartridges.

All this hinges on us being able to effectively "file/print" DNA molecules. It's fun to watch technology accelerate, I am one excited geek.

You make toying with genes sound like fun. But this field is rife with potential for bad unforseen consequences.

Suppose somebody designs a breed of dog that can run twice as fast as a greyhound. Thousands of the cute critters are bred, but it turns out that this breed also invariably develops severe osteoarthritis at three years of age. A great deal of suffering has just resulted from somebody's "toying".

Things get worse when you start to mix in human genes. At what point should you start to accord hu

I have not studied extensively DNA, proteins, or even simple chemistry. I believe, however, that these things can be modeled, and explored. We'll find some self-organizing results, and self-distroying results. It does take quite the balance for a creature to exist -- take away the sequence for the high-affinity choline receptor, and you get a creature that just doesn't work all that well. This type of knock-out mouse will be fine until it starts breathing on it's own, and not having that particular receptor

Your water is dangerous too! Do you have filters on your water tap? I drink straight from the tap.

Hell, if I could find out which GM foods were, I'd like to try 'em. Who cares if it's a bigger tomato, and is perhaps jucier and more tasty? I do, and that's what I think I want in a tomato, not a dinky little spotted nasty rotted thing -- which is what I see alot as an excuse for a natural tomato.

Selective breeding has been going on for longer than I care to speculate. And how bad is that? A bigger, tasti

Well let's see: it has to grab your initial attention by being odd looking enough to be interesting and be annoying enough to immediately drive you away and wish you'd never seen it, while not allowing you to easily ignore it. Even when it's just out of sight, you know it's still there and it still bothers you.

I think it must have something to do with the suggested link between light autism and hard core geekery.